Alternatives to HyperProtein
Compare HyperProtein alternatives for your business or organization using the curated list below. SourceForge ranks the best alternatives to HyperProtein in 2025. Compare features, ratings, user reviews, pricing, and more from HyperProtein competitors and alternatives in order to make an informed decision for your business.
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1
Evo 2
Arc Institute
Evo 2 is a genomic foundation model capable of generalist prediction and design tasks across DNA, RNA, and proteins. It utilizes a frontier deep learning architecture to model biological sequences at single-nucleotide resolution, achieving near-linear scaling of compute and memory relative to context length. Trained with 40 billion parameters and a 1 megabase context length, Evo 2 processes over 9 trillion nucleotides from diverse eukaryotic and prokaryotic genomes. This extensive training enables Evo 2 to perform zero-shot function prediction across multiple biological modalities, including DNA, RNA, and proteins, and to generate novel sequences with plausible genomic architecture. The model's capabilities have been demonstrated in tasks such as designing functional CRISPR systems and predicting disease-causing mutations in human genes. Evo 2 is publicly accessible via Arc's GitHub repository and is integrated into the NVIDIA BioNeMo framework. -
2
Profluent
Profluent
Profluent's platform revolutionizes protein design by integrating advanced AI with in-house wet-lab capabilities, enabling the creation of proteins either inspired by nature or reimagined from scratch. This holistic approach allows for precise, adaptable, and scalable solutions to complex biological challenges, delivering results that redefine what's possible with proteins. Profluent's foundation models push the frontier of protein design beyond the limitations of random discovery, facilitating the optimization of multiple attributes simultaneously, accessing greater sequence diversity, and enabling novel functionalities. By extrapolating into new protein spaces, Profluent offers unique possibilities beyond natural or patented proteins, making it cheaper, easier, and feasible for partners to achieve commercial success. Profluent's capabilities are built on a commitment to scientific rigor, leveraging diverse datasets and advanced AI to tackle challenges. -
3
Evo Designer
Arc Institute
Evo Designer is an advanced tool developed by the Arc Institute, leveraging the capabilities of the Evo 2 genomic foundation model to facilitate DNA sequence generation and analysis. This platform enables users to input nucleotide sequences or specify organisms, prompting the model to generate corresponding DNA sequences. It provides comprehensive annotations of coding regions and, for prokaryotic sequences, offers 3D protein visualizations utilizing ESMFold. Additionally, Evo Designer evaluates sequences by scoring their perplexity and per-nucleotide entropy, assisting researchers in assessing sequence complexity and variability. The underlying Evo 2 model is trained on over 9 trillion nucleotides from a diverse array of prokaryotic and eukaryotic genomes, employing a deep learning architecture that models biological sequences at single-nucleotide resolution with a context window extending up to 1 million tokens. -
4
Swiss-PdbViewer
Swiss-PdbViewer
Swiss-PdbViewer (aka DeepView) is an application that provides a user-friendly interface allowing to analysis of several proteins at the same time. The proteins can be superimposed in order to deduce structural alignments and compare their active sites or any other relevant parts. Amino acid mutations, H-bonds, angles, and distances between atoms are easy to obtain thanks to the intuitive graphic and menu interface. Swiss-PdbViewer (aka DeepView) has been developed since 1994 by Nicolas Guex. Swiss-PdbViewer was initially tightly linked to SWISS-MODEL, an automated homology modeling server developed within the Swiss Institute of Bioinformatics (SIB) at the Structural Bioinformatics Group at the Biozentrum in Basel. However, the SWISS-MODEL web interface evolved to a point where it is now possible to use it directly for advanced modeling. Maintaining a direct interface with Swiss-PdbViewer is too complex and no longer supported. -
5
BioNeMo
NVIDIA
BioNeMo is an AI-powered drug discovery cloud service and framework built on NVIDIA NeMo Megatron for training and deploying large biomolecular transformer AI models at a supercomputing scale. The service includes pre-trained large language models (LLMs) and native support for common file formats for proteins, DNA, RNA, and chemistry, providing data loaders for SMILES for molecular structures and FASTA for amino acid and nucleotide sequences. The BioNeMo framework will also be available for download for running on your own infrastructure. ESM-1, based on Meta AI’s state-of-the-art ESM-1b, and ProtT5 are transformer-based protein language models that can be used to generate learned embeddings for tasks like protein structure and property prediction. OpenFold, a deep learning model for 3D structure prediction of novel protein sequences, will be available in BioNeMo service. -
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MEGA
MEGA
MEGA (Molecular Evolutionary Genetics Analysis) is a powerful and user-friendly software suite designed for analyzing DNA and protein sequence data from species and populations. It facilitates both automatic and manual sequence alignment, phylogenetic tree inference, and evolutionary hypothesis testing. MEGA supports a variety of statistical methods including maximum likelihood, Bayesian inference, and ordinary least squares, making it an essential tool for comparative sequence analysis and understanding molecular evolution. MEGA offers advanced features such as real-time caption generation to help explain the results and methods used in analysis and the maximum composite likelihood method for estimating evolutionary distances. The software is equipped with robust visual tools like the alignment/trace editor and tree explorer and supports multi-threading for efficient processing. MEGA can be run on multiple operating systems, including Windows, Linux, and macOS.Starting Price: Free -
7
LigPlot+
EMBL-EBI
LigPlot+ is a successor to our original LIGPLOT program for the automatic generation of 2D ligand-protein interaction diagrams. It is run from an intuitive java interface that allows on-screen editing of the plots via mouse click-and-drag operations. In addition to the new interface, the program includes several major enhancements over the old version. When two or more ligand-protein complexes are sufficiently similar, LigPlot+ can automatically display their interaction diagrams either superposed or side by side. Any conserved interactions are highlighted. The LigPlot+ suite also now includes an update of the original DIMPLOT program for plotting protein-protein or domain-domain interactions. Users can flexibly select the interface of interest and DIMPLOT will then generate a diagram showing the residue-residue interactions across the interface. To assist in interpretation, the residues in one of the interfaces can be optionally displayed in sequence order. -
8
3decision
Discngine
3decision® is a cloud-based protein structure repository designed for comprehensive structural data management and advanced analytics, enabling small molecule and biologics discovery teams to accelerate structure-based drug design. It centralizes and standardizes experimental and in-silico protein structures from public sources like RCSB PDB and AlphaFoldDB, as well as proprietary data, supporting formats like PDBx/mmCIF and ModelCIF. This ensures easy access to X-Ray, NMR, cryo-EM, and modeled structures, fostering collaboration and enhancing research efforts. Beyond storage, 3decision® enriches entries with metadata and sequence information, including protein-ligand interactions, antibody annotations, and binding site details. Advanced analytical tools identify druggable sites, assess off-target risks, and enable binding site comparisons, transforming vast structural data into actionable knowledge. Its cloud-based platform facilitates collaboration among research teams. -
9
AlphaFold
DeepMind
These exquisite, intricate machines are proteins. They underpin not just the biological processes in your body but every biological process in every living thing. They’re the building blocks of life. Currently, there are around 100 million known distinct proteins, with many more found every year. Each one has a unique 3D shape that determines how it works and what it does. But figuring out the exact structure of a protein remains an expensive and often time-consuming process, meaning we only know the exact 3D structure of a tiny fraction of the proteins known to science. Finding a way to close this rapidly expanding gap and predict the structure of millions of unknown proteins could not only help us tackle disease and more quickly find new medicines but perhaps also unlock the mysteries of how life itself works. -
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Eidogen-Sertanty Target Informatics Platform (TIP)
Eidogen-Sertanty
Eidogen-Sertanty's Target Informatics Platform (TIP) is the world's first structural informatics system and knowledgebase that enables researchers with the ability to interrogate the druggable genome from a structural perspective. TIP amplifies the rapidly expanding body of experimental protein structure information and transforms structure-based drug discovery from a low-throughput, data-scarce discipline into a high-throughput, data-rich science. Designed to help bridge the knowledge gap between bioinformatics and cheminformatics, TIP supplies drug discovery researchers with a knowledge base of information that is both distinct from and highly complementary to information furnished by existing bio- and cheminformatics platforms. TIP's seamless integration of structural data management technology with unique target-to-lead calculation and analysis capabilities enhances all stages of the discovery pipeline. -
11
Orbit BioSequence
Questel
Orbit BioSequence by Questel is a powerful IP intelligence software specifically designed to help researchers, patent professionals, and biotech companies analyze and manage biological sequence data within the intellectual property (IP) landscape. It offers an advanced solution for searching, analyzing, and monitoring nucleotide and protein sequences found in patent documents, giving users unprecedented access to sequence information critical for innovation and competitive analysis. Orbit BioSequence allows users to perform highly accurate similarity and identity searches across global patent databases, helping organizations identify existing patents, avoid infringement risks, and uncover licensing or partnership opportunities. It also integrates cutting-edge search algorithms and curated datasets to ensure precision and relevance in search results. -
12
CryoTrack
CryoTrack
CryoTrackIMS is a complete software package - ideal for molecular biology, cell banks, cellular biology, clinical samples, biorepository, biobanking, biochemistry, immunology and protein labs, high-throughput screening, QA, IVF labs and core labs and facilities. Create any box, plate or pie configuration - select rows and columns or select a Pie configuration - your box is created in seconds ready to input data. Inventory of valuable biological samples and specimen is critical for basic research and biotech business. Keeping track of large numbers and types of samples (DNA, RNA, plasmids, clones, proteins, peptides, probes, antibodies, enzymes, specimen, tissues, cell lines and more) and where they are and their precise location is a nightmare and daunting task for many that cost a great deal not only in monetary terms but also leads to frustrations and time loss. CryoTrack offers a complete solution for individual labs in universities, clinics, biotech and pharmaceutical companies. -
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GeoMx Digital Spatial Profiler (DSP)
nanoString
Quickly resolve tissue heterogeneity and the complexity of microenvironments with the GeoMx Digital Spatial Profiler (DSP), the most flexible and robust spatial multi-omic platform for analysis of FFPE and fresh frozen tissue sections. GeoMx is the only spatial biology platform that non-destructively profiles the expression of RNA and protein from distinct tissue compartments and cell populations with an automated and scalable workflow that integrates with standard histology staining. Spatially profile the whole transcriptome and 570+ protein targets separately or simultaneously from your choice of sample inputs: whole tissue sections, tissue microarrays (TMAs), or organoids. Make GeoMx DSP your spatial biology platform of choice for biomarker discovery and hypothesis testing. Decide where to draw the line and let the tissue be your guide with biology-driven profiling that empowers you to choose the tissue microenvironments and cell types that matter most to you. -
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Avogadro
Avogadro
Avogadro is an advanced molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. It offers flexible high quality rendering and a powerful plugin architecture. Avogadro is a free, open-source molecular editor and visualization tool, designed for use on Mac, Windows, and Linux in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. It offers flexible high quality rendering and a powerful plugin architecture. -
15
MolView
MolView
MolView is an intuitive, Open-Source web application to make science and education more awesome! MolView is mainly intended as a web-based data visualization platform. You can use MolView to search through different scientific databases including compound databases, protein databases and spectral databases, and view records from these databases as interactive visualizations using WebGL and HTML5 technologies. This web application is built on top of the JavaScript libraries and online services listed below. The Virtual Model Kit has been a source of inspiration for the birth of this project.Starting Price: Free -
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Genedata Biologics
Genedata
Genedata Biologics® streamlines discovery of biotherapeutics including bispecifics, ADCs, TCRs, CAR-Ts, and AAVs. The most widely adopted platform across the industry, it integrates all discovery workflows so you can focus on true innovation. Accelerate research with a first-in-class platform uniquely designed from the start to digitalize biotherapeutic discovery. The platform facilitates complex R&D processes by designing, tracking, testing, and assessing novel biotherapeutics drugs. It works with any format, from antibodies, bi- or multi-specifics, ADCs, novel scaffolds, and therapeutic proteins, to engineered therapeutic cell lines such as TCRs and CAR-T cells. Acting as a central end-to-end data backbone, Genedata Biologics integrates all R&D processes, from library design and immunizations, selections and panning, molecular biology, screening, protein engineering, expression, purification, and protein analytics, to candidate developability and manufacturability assessments. -
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QSimulate
QSimulate
QSimulate offers a suite of quantum simulation platforms that leverage quantum mechanics to solve complex, industrial-scale problems in life sciences and materials science. The QSP Life platform provides unique quantum-powered methods for drug discovery and optimization, enabling first-of-a-kind quantum simulations of ligand-protein interactions applicable throughout the computational drug discovery process. The QUELO platform performs hybrid quantum/classical free energy calculations, offering users the ability to run relative free energy calculations using the free energy perturbation (FEP) approach. Additionally, QSimulate's technology enables groundbreaking advances in quantum mechanics/molecular mechanics (QM/MM) simulations for large protein modeling. For materials science, the QSP Materials platform democratizes quantum mechanical simulations, allowing experimentalists to automate complex workflows without the need for specialization. -
18
Ascalaph Designer
Agile Molecule
Ascalaph Designer is a general-purpose program for molecular dynamic simulations. Under a single graphical environment are represented as their own implementation of molecular dynamics as well as the methods of classical and quantum mechanics of popular programs. Molecular geometry optimization with conjugate gradient methods. Shows molecular models in separate windows. Each window has two cameras, which allow the model to be simultaneously visualized from two sides and in different graphic modes. The subwindow can be opened by dragging the splitter in the right corner of each graphical window. Clicking on an atom or bond with the left mouse button slightly changes their color and a brief info about the picked object appears in the status bar. The wire-frame style is convenient for large molecules, particularly, proteins. Drawing is very fast for this style. Finally, CPK wire frame combines the properties of several above styles.Starting Price: Free -
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BIOVIA Discovery Studio
Dassault Systèmes
Today’s biopharmaceutical industry is marked by complexity: growing market demands for improved specificity and safety, novel treatment classes and more intricate mechanisms of disease. Keeping up with this complexity requires a deeper understanding of therapeutic behavior. Modeling and simulation methods provide a unique means to explore biological and physicochemical processes down to the atomic level. This can guide physical experimentation, accelerating the discovery and development process. BIOVIA Discovery Studio brings together over 30 years of peer-reviewed research and world-class in silico techniques such as molecular mechanics, free energy calculations, biotherapeutics developability and more into a common environment. It provides researchers with a complete toolset to explore the nuances of protein chemistry and catalyze discovery of small and large molecule therapeutics from Target ID to Lead Optimization. -
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YASARA
YASARA
YASARA is a molecular graphics, modeling, and simulation program for Windows, Linux, MacOS, and Android developed in 1993, that finally makes it really easy to answer your questions. With an intuitive user interface, photorealistic graphics, and support for affordable virtual reality headsets, shutter glasses, autostereoscopic displays, and input devices, YASARA creates a new level of interaction with the 'artificial reality', that allows you to focus on your goal and forget about the details of the program. YASARA is powered by PVL (Portable Vector Language), a new development framework that provides performance way above traditional software. PVL allows you to visualize even the largest proteins and enables true interactive real-time simulations with highly accurate force fields on standard PCs, making use of GPUs if available. You can push and pull molecules around and work with dynamic models instead of static pictures.Starting Price: Free -
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IPA can also be used for analysis of small-scale experiments that generate gene and chemical lists. IPA allows searches for targeted information on genes, proteins, chemicals, and drugs, and building of interactive models of experimental systems. Data analysis and search capabilities help in understanding the significance of data, specific targets, or candidate biomarkers in the context of larger biological or chemical systems. The software is backed by the Ingenuity Knowledge Base of highly structured, detail-rich biological and chemical findings. Learn more about QIAGEN Ingenuity Pathway Analysis (IPA). Comparison Analysis determines the most significant pathways, upstream regulators, diseases, biological functions, and more, across time points, dose, or other conditions.
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22
Promethium
Promethium
Promethium is a GPU-powered chemistry simulation platform designed to accelerate drug and materials development by enabling faster and more accurate quantum chemistry calculations. Built from the ground up for NVIDIA datacenter GPUs like A100, it employs novel QC Ware streaming algorithms to achieve unprecedented computational speed and high throughput-to-power consumption ratios. It supports density functional theory calculations on systems with up to 2,000 atoms, allowing simulations of large molecular systems that are not feasible with legacy CPU-powered ab initio codes. For instance, a single-point calculation of a 2,056-atom protein can be completed in 14 hours on a single GPU. Promethium offers a range of capabilities, including single-point energy calculations, geometry optimization, conformer search, torsion scan, reaction path optimization, transition state optimization, interaction energy computations, and relaxed potential energy surface scans.Starting Price: $30 per hour -
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ProteinOS
Protein Platform
The Protein Platform is a collection of desktop software, web-based software, hardware, 3rd party services, and cloud infrastructure. The main customer facing component is our self updating, distributed windows desktop application ProteinOS which facilitates the efficient handling of customer order workflow for Wild Game Processors. Our kiosks consist of MiniPCs, POS Receipt Printers, Thermal Label Printers, RFID, mobile pc carts with onboard UPS for use away from a wall outlet, and proprietary hardware fingerprinting tying your hardware to your organization allowing fast and rigorously secure communication with Protein Platform's cloud infrastructure. Orders are assigned an RFID tag which when scanned at each station brings up the data required at that station. Customer notifications (SMS, Voice, Email) and customer invoices are automated and customizable. Quick views of current demand, freezer capacity, pending orders, and orders ready for pickup help keep your business moving!Starting Price: $100/month -
24
PDQuest
Bio-Rad Laboratories
PDQuest 2-D analysis software, version 8.0, offers comprehensive and flexible 2-D gel electrophoretic analysis. Choose PDQuest Basic for simple 2-D gel analysis or PDQuest Advanced for the latest available features for 2-D gel-based expression proteomics studies. Whether you choose the basic or advanced version, the sophisticated analysis tools reveal subtle differences among 2-D gels. Powerful auto-matching algorithms quickly and accurately match gels with little or no manual intervention. PDQuest software's flexible annotation features make it a useful tool to establish a centralized information repository, which allows virtually any type of characterizing data to be linked to each spot on a master gel image. It is easy to view and share information associated with identified proteins. Spot cutting configurations for high accuracy, high throughput, and flexibility in protein identification experiments. -
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CAI Provisions
CAI Software
Choosing the right business management software for your protein or specialty food processing and distribution business can be challenging. That’s because some packages don’t offer everything you need, while others are either too expensive to purchase and or just too complex to operate. Whether you’re a meat/protein processor requiring portion control and custom cutting capabilities or a specialty food processor using bills of materials or recipes to cook, bake, fry, mix or assemble your products and looking to gain better control and visibility over your processes, Provisions gives you the tools to improve efficiency, reduce business costs and maximize margins. Each of our software solutions has a specialized team of professionals dedicated to supporting you during and after your implementation. We go above and beyond to ensure your software runs smoothly and provides value every day.Starting Price: $15000.00/one-time -
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BaseSpace Sequence Hub
Illumina
Data management and simplified bioinformatics for labs getting started and for rapidly scaling next-generation sequencing (NGS) operations. As a key component of the BaseSpace Suite, BaseSpace Sequence Hub is a direct extension of your Illumina instruments. Encrypted data flow from the instrument into BaseSpace Sequence Hub, enabling you to manage and analyze your data easily with a curated set of analysis apps. BaseSpace Sequence Hub is powered by Amazon Web Services (AWS). Offers a security-first environment. Enables you to set up runs and monitor instrument run quality. Promotes efficiency by converting sequencing data to a standard format and streaming directly to the cloud. Provides access to computing resources without the capital expenditure of in-house infrastructure. Increases organizational productivity with easy access to a multitude of genomic analysis apps (provided by you, Illumina, or third parties). -
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VeraChem
VeraChem
VeraChem LLC was founded in 2000 to advance the state of the art in computer-aided drug discovery and molecular design by developing computational chemistry methods that are based on cutting-edge basic science but are also applicable in applied science research settings. Efficient high-performance software implementations of these methods coupled with comprehensive user support are a central company strategy for product development. Current VeraChem software capabilities include protein-ligand and host-guest binding affinity prediction, fast calculation of accurate partial atomic charges for drug-like compounds, computation of energies and forces with all the commonly used empirical force fields, automatic generation of alternate resonance forms of drug-like compounds, conformational search with the powerful Tork algorithm, and automatic detection of topological and 3D molecular symmetries. VeraChem’s software packages are constructed from a modular code base. -
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quattro/CM
quattro research
quattro research GmbH is an interdisciplinary team of scientists and IT specialists. We develop innovative solutions and products for our customers from the life science , pharma and chemistry industries. Integration and separation of databases and intellectual property after mergers and spin-offs respectively. Biological and chemical registration systems, including complex proteins, supporting the HELM notation. Scientists working with antibodies, antibodydrug-conjugates, large peptides, RNA molecules or any other biomolecule need appropriate software solutions. quattro research offers solutions for registration and management of biomolecules based on the open HELM Notation & Editor. -
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FutureHouse
FutureHouse
FutureHouse is a nonprofit AI research lab focused on automating scientific discovery in biology and other complex sciences. FutureHouse features superintelligent AI agents designed to assist scientists in accelerating research processes. It is optimized for retrieving and summarizing information from scientific literature, achieving state-of-the-art performance on benchmarks like RAG-QA Arena's science benchmark. It employs an agentic approach, allowing for iterative query expansion, LLM re-ranking, contextual summarization, and document citation traversal to enhance retrieval accuracy. FutureHouse also offers a framework for training language agents on challenging scientific tasks, enabling agents to perform tasks such as protein engineering, literature summarization, and molecular cloning. Their LAB-Bench benchmark evaluates language models on biology research tasks, including information extraction, database retrieval, etc. -
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StrainControl Laboratory Manager
DNA Globe
Store strains, cell-lines, proteins, plasmids, oligos, chemicals, inventories etc in StrainControl. You can customize all field titles to fit your lab needs. It has never been easier to manage lab items. Try our free version today and get a feeling how StrainControl can help you and the other members in the lab. No need to ask for the same thing twice. Your lab will be running smoother than ever. Share your StrainControl database with other lab members over your computer network. With user management you can create various accounts to protect your database. StrainControl is maximized with features that will help you manage everything in the lab. Manage strains, cell-lines, proteins, plasmids, oligos, chemicals, inventories etc. Share your database on a network. Rename modules, column and text fields. Hide columns that are not used. Create user accounts (read/write/admin etc). Import or export using user-friendly guides. Link files (protocols, images etc) to database.Starting Price: $299 one-time payment -
31
Geneious
Geneious
Geneious Prime makes bioinformatics accessible by transforming raw data into visualizations that make sequence analysis intuitive and user-friendly. Simple sequence assembly and easy editing of contigs. Automatic annotation for gene prediction, motifs, translation, and variant calling. Genotype microsatellite traces with automated ladder fitting and peak calling and generates tables of alleles. Beautiful visualizations of annotated genomes and assemblies are displayed in a highly customizable sequence view. Powerful SNP variants analysis, simple RNA-Seq expression analysis, and amplicon metagenomics. Design and test PCR and sequencing primers and create your own searchable primer database. Geneious Biologics is a flexible, scalable, and secure way to streamline your antibody analysis workflows, create high-quality libraries and select the optimal therapeutic candidates.Starting Price: $1,280 per year -
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ChemSketch
ACD/Labs
Comprehensive molecular structure drawing and naming. Draw chemical structures and communicate your science. -
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Geneyx
Geneyx
Geneyx Analysis is a comprehensive solution for next-generation sequencing (NGS) data that can scale the process of FASTQ to clinical reports for hospital and commercial labs. This advanced platform integrates machine learning and AI-based features to identify novel biomedical insights, while also improving diagnostic yields and turnaround times. By providing a fully transparent and intuitive solution, Geneyx Analysis enables clinicians and researchers to have complete control over data analysis and alleviates the complexities of regulating in-house bioinformatics pipelines. Protocols can be fully customized to accommodate gene panels, exomes, and genomes, and our comprehensive annotation engine supports the analysis of all genetic variants including structural and copy number variations as well as regulatory elements. Together, Geneyx Analysis automates the diagnostic process from sequencer to report, while creating a comprehensive resource for novel variant discovery. -
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Dotmatics
Dotmatics
Dotmatics is the global leader in R&D scientific software that connects science, data, and decision-making. Combining a workflow and data platform with best-of-breed applications, we offer the first true end-to-end solutions for biology, chemistry, formulations, data management, flow cytometry, and more. Trusted by more than 2 million researchers from the world’s leading biopharma, chemicals and materials enterprises, and academic institutions, we are dedicated to working with the scientific community to help make the world a healthier, cleaner and safer place to live. Learn more about our platform and products, including GraphPad Prism, Geneious, SnapGene, Protein Metrics, LabArchives, and more. -
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Sapio Scientific Data Cloud
Sapio Sciences
Sapio Scientific Data Cloud is a science-aware scientific data management system that unifies and contextualizes all your laboratory data, assay results, instrument outputs, archives, and third-party ELN/LIMS records into a single, searchable platform without any coding. It supports automated data capture and parsing from over 200 instrument adaptors, semantic search powered by ontologies, built-in charting, and advanced neural-network analytics (ANOVA, best-response curves, 4/5 PL curves, flow-cytometry gating), and AI-driven insights. Secure, role-based access and data archiving keep sensitive information safe, while protein, molecule, plasmid, and system-wide viewers let scientists explore results interactively. Deep integration with Sapio LIMS and ELN systems automatically associates data with samples, experiments, and entities. -
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Partek Flow
Partek
Partek bioinformatics software delivers powerful statistical and visualization tools in an easy-to-use interface. Researchers of all skill levels are empowered to explore genomic data quicker and easier than ever before. We turn data into discovery®. Pre-installed workflows and pipelines in our intuitive point-and-click interface make sophisticated NGS and array analysis attainable for any scientist. Custom and public statistical algorithms work in concert to easily and precisely distill NGS data into biological insights. Genome browser, Venn diagrams, heat maps, and other interactive visualizations reveal the biology of your next-generation sequencing and array data in brilliant color. Our Ph.D. scientists are always just a phone call away and ready to help with your NGS analysis any time you have questions. Designed specifically for the compute-intensive needs of next-generation sequencing applications with flexible installation and user management options. -
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Genome Analysis Toolkit (GATK)
Broad Institute
Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. The GATK is the industry standard for identifying SNPs and indels in germline DNA and RNAseq data. Its scope is now expanding to include somatic short variant calling and to tackle copy number (CNV) and structural variation (SV). In addition to the variant callers themselves, the GATK also includes many utilities to perform related tasks such as processing and quality control of high-throughput sequencing data and bundles the popular Picard toolkit. These tools were primarily designed to process exomes and whole genomes generated with Illumina sequencing technology, but they can be adapted to handle a variety of other technologies and experimental designs.Starting Price: Free -
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QIAGEN CLC Genomics Workbench
QIAGEN Digital Insights
QIAGEN CLC Genomics Workbench is a powerful solution that works for everyone, no matter the workflow. Cutting-edge technology and unique features and algorithms widely used by scientific leaders in industry and academia make it easy to overcome challenges associated with data analysis. User-friendly bioinformatics software solutions allow for comprehensive analysis of your NGS data, including de novo assembly of whole genomes and transcriptomes, resequencing analysis (WGS, WES and targeted panel support), variant calling, RNA-seq, ChIP-seq and DNA methylation (bisulfite sequencing analysis). Analyze your RNA-seq and small RNA (miRNA, lncRNA) data with easy-to-use transcriptomics workflows for differential expression analysis at gene and transcript levels. QIAGEN CLC Genomics Workbench is developed to support a wide range of NGS bioinformatics applications. -
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BIOVIA
Dassault Systèmes
BIOVIA solutions create an unmatched scientific management environment that can help science-based organizations create and connect biological, chemical and material innovations to improve the way we live. The industry-leading BIOVIA portfolio is focused on integrating the diversity of science, experimental processes and information requirements end-to-end across research, development, QA/QC and manufacturing. Capabilities over the areas of Scientific Informatics, Molecular Modeling/Simulation, Data Science, Laboratory Informatics, Formulation Design, BioPharma Quality & Compliance and Manufacturing Analytics. BIOVIA is committed to enhancing and speeding innovation, increasing productivity, improving quality and compliance, reducing costs and accelerating product development for customers in multiple industries. Manage and connect scientific innovation processes and information across the product lifecycle. -
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Galaxy
Galaxy
Galaxy is an open source, web-based platform for data-intensive biomedical research. If you are new to Galaxy start here or consult our help resources. You can install your own Galaxy by following the tutorial and choosing from thousands of tools from the tool shed. This instance of Galaxy is utilizing infrastructure generously provided by the Texas Advanced Computing Center. Additional resources are provided primarily on the Jetstream2 cloud via ACCESS, and with support from the National Science Foundation. Quantify, visualize, and summarize mismatches in deep sequencing data. Build maximum-likelihood phylogenetic trees. Phylogenomic/evolutionary tree construction from multiple sequences. Merge matching reads into clusters with TN-93. Remove sequences from a reference that are within a given distance of a cluster. Perform maximum-likelihood estimation of gene essentiality scores.Starting Price: Free -
41
AutoDock
AutoDock
AutoDock is a suite of automated docking tools. It is designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure. Over the years, it has been modified and improved to add new functionalities, and multiple engines have been developed. Current distributions of AutoDock consist of two generations of software: AutoDock 4 and AutoDock Vina. More recently, we developed AutoDock-GPU, an accelerated version of AutoDock4 that is hundreds of times faster than the original single-CPU docking code. AutoDock 4 actually consists of two main programs: autodock performs the docking of the ligand to a set of grids describing the target protein; autogrid pre-calculates these grids. In addition to using them for docking, the atomic affinity grids can be visualized. This can help, for example, to guide organic synthetic chemists design better binders. -
42
Aurora Drug Discovery
Aurora Fine Chemicals
Aurora employs quantum mechanics, thermodynamics, and an advanced continuous water model for solvation effects to calculate ligand´s binding affinities. This approach differs dramatically from scoring functions that are commonly used for binding affinity predictions. By including the entropy and aqueous electrostatic contributions in to the calculations directly, Aurora algorithms produce much more accurate and robust values of binding free energies. Interaction of a ligand with a protein is characterized by the value of binding free energy. The free energy (F) is the thermodynamic quantity that is directly related to experimentally measurable value of inhibition constant (IC50) and depends on electrostatic, quantum, aqueous solvation forces, as well as on statistical properties of interacting molecules. There are two major contributing quantities leading to non-additivity in F: 1) the electrostatic and solvation energy and 2) the entropy. -
43
SILCS
SilcsBio
Site-Identification by Ligand Competitive Saturation (SILCS) generates 3D maps (FragMaps) of interaction patterns for chemical functional groups with your target molecule. Site-Identification by Ligand Competitive Saturation (SILCS) generates 3D maps (FragMaps) of interaction patterns for chemical functional groups with your target molecule. SILCS reveals intricacies of dynamics and provides tools to optimize ligand scaffolds using qualitative and quantitative binding pockets insights allowing more rapid and effective drug design. SILCS uses multiple small molecule probes with various functional groups, explicit solvent modeling, and target molecule flexibility to perform protein target mapping. Visualize favorable interactions with the target macromolecule. Gain insights to design better ligands with optimally placed functional groups. -
44
NLMatics
NLMatics
Easiest way to extract data points from unstructured text. Simultaneously search through research reports, prospectus, customer requests or feedback to extract, track and analyze meaningful, custom defined data points. Access 100+ unique data points for your investment & risk management strategy. Search and create custom data sets from EDGAR and other public or private sources. Streamline your deal underwriting process. Streamline your capital markets and structured finance legal flow. Instantly extract 100+ data points to categorize, compare and collaborate with your clients. Deconstruct unstructured text in PubMed and clinical trial data into diseases, genes, proteins, symptoms & more. Get all your research in a single place. Bring in research from any source into your workspaces using our Chrome plug-in. Make digital PDFs to machine readable. JSON and HTML output with detailed section hierarchy, multi-level tables, lists, header, footer and watermarks removed. -
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MolPad
MolPad
MolPad integrates an interactive chemistry sketcher into any online learning platform. Build open questions about molecular structure and organic chemistry that go beyond just recognizing the right answer. Discover how MolPad can enrich online chemistry education by providing a low code environment for creating dynamic content and smart assessment. With MolPad, we have developed several solutions for interactive and intuitive drawing of structural formulas, enabling the student to practice with topics like chemical naming, functional groups, and Lewis structures in a digital environment. By providing smart feedback based on specific errors, the student can gain more insight than with multiple choice questions. -
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Mass Dynamics
Mass Dynamics
Discover biological biomarkers, create insights into disease mechanisms, discover new drugs or identify changes in protein levels from a set of carefully designed experiments. We’ve made it easy to start unlocking the power of MS and Proteomics so you can focus on the biological complexity and move closer to the moment of discovery. Our automated and repeatable workflow allows for quicker experiment startup and turnaround times, giving you the control and flexibility to make and act on decisions in the moment. Allowing you to focus on biological insights and human-to-human collaboration, our proteomics data processing workflow is built to scale, repeatedly. We’ve pushed heavy and repetitive processing to the cloud, enabling a seamless and enjoyable experience. Our intelligent Proteomics workflow seamlessly integrates complex moving parts to enable larger experiments to be processed and analyzed with ease. -
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Tox Suite
ACD/Labs
Calculate drug toxicity and safety endpoints to reduce attrition rates of molecular entities that are unlikely to succeed to nomination as a drug candidate, direct new compound synthesis, and focus animal testing requirements. -
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MeAgain
MeAgain
MeAgain is a personalized health app designed to support users on their GLP-1 journey with confidence and clarity. It offers tools to track protein, water, and fiber goals, as well as reminders and trackers for GLP-1 injections. The app also helps monitor weight goals and side effects, providing a comprehensive approach to health management. Users appreciate its ease of use and features like barcode scanning and photo recognition for food logging. MeAgain empowers individuals to reclaim their health by turning goals into sustainable habits. With supportive feedback and progress tracking, the app helps users stay motivated throughout their journey. MeAgain is designed specifically for people on GLP-1 medications like Ozempic®, Wegovy®, Mounjaro®, Zepbound®, generics and compounds. MeAgain helps you build and stay on track with your new habits, manage side effects, and ensure you feel like you again soon.Starting Price: Free -
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QuartzBio
QuartzBio
QuartzBio is a precision-medicine intelligence platform designed to transform how clinical development and translational research teams work by providing a unified data ecosystem where biospecimen, biomarker, and clinical data can be ingested, harmonized, explored, and interrogated via conversational AI. Powered by its Precision Medicine AI Agent Platform, QuartzBio includes key solutions like Sample Intelligence, which offers a 360° view of biospecimen lifecycles from collection to long-term storage and uses automated logistics, stability monitoring and data-reconciliation tools; and Biomarker Intelligence, which delivers unified ingestion of assay data across DNA, RNA, protein and cell-based modalities, a no-code data-mapper, global search, dashboards, visual analytics and genomic/cytometry modules; additionally, the Agent Intelligence layer enables natural-language queries across the data asset so stakeholders. -
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SnapGene
SnapGene
Accurately design and simulate cloning procedures. Test complicated projects, catch errors before they happen, and obtain the right constructs the first time. Cloning is easier when you can see what you are doing. The intuitive interface offers you unparalleled visibility into your work, simplifying often complex tasks. SnapGene automates documentation, so you don’t have to. See and share every sequence edit and cloning procedure that led to your final plasmid. Improve your core molecular biology procedures, and improve your results. Master SnapGene and key concepts in cloning with our new online learning center, SnapGene Academy. Containing over 50 video tutorials taught by scientific experts, SnapGene Academy helps you advance your skills across multiple molecular biology courses. SnapGene 7.2 provides a new visualization of primer homodimer structures and enhancements to file management, allowing tabs to be organized in multiple windows using drag and drop.Starting Price: $295 per year
